R Notebook zScale

library(stringi)
library(Peptides)
library(bio3d)
setwd("D:/Batches_Sim/Batch_3")

Warning: The working directory was changed to D:/Batches_Sim/Batch_3 inside a notebook chunk. The working directory will be reset when the chunk is finished running. Use the knitr root.dir option in the setup chunk to change the working directory for notebook chunks.

files <- list.files(pattern="EKB1m.pdb$", recursive = TRUE)
files <- files[order(nchar(files), files)]
files <- paste0("D:/Batches_Sim/Batch_3/", files)

sequences <- list()
for (file in files){
  pdb <- read.pdb(file)
  seq <- pdbseq(pdb, inds = NULL, aa1 = TRUE)
  sequences[[length(sequences) + 1 ]] <- seq
}

print(length(sequences))

[1] 312

Scales_variables <- list()
for (i in sequences){
  new_element <- (aaDescriptors(i))
  Scales_variables[[length(Scales_variables) + 1]] <- new_element
}

library(readxl)
library(writexl)
exceldata <- read_excel("C:\\Users\\venan\\OneDrive\\Desktop\\Work\\Scripts_for_Nick\\ML\\Dataset_Nick_heading.xlsx")
dfdata <- data.frame(exceldata)
df_scales <- as.data.frame(Scales_variables)
df_scales

col_names <- list()
for (i in names(df_scales)){
  new_name <- i
  col_names[[length(col_names) + 1]] <- new_name
}
col_sum <- data.frame(colSums(df_scales))
new_df_col_names <- col_names[1:66]

indeces <- grep("PP1", colnames(df_scales))
df <- data.frame()
for (i in indeces){
    df <- rbind(df, col_sum[i:(i+65),])
  }
df

names(df) <- new_df_col_names

new_df <- cbind(dfdata, df)
write_xlsx(new_df, "C:\\Users\\venan\\OneDrive\\Desktop\\Work\\Scripts_for_Nick\\ML\\new_df_66.xlsx")

new_df

Error: object 'new_df' not found